Feat: Add integrity check to cli

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added the integrity check to the jabkit cli application. [#13848](https://github.com/JabRef/jabref/issues/13848)
 - We added support for Cygwin-file paths on a Windows Operating System. [#13274](https://github.com/JabRef/jabref/issues/13274)
 - We fixed an issue where "Print preview" would throw a `NullPointerException` if no printers were available. [#13708](https://github.com/JabRef/jabref/issues/13708)
 - We added the option to enable the language server in the preferences. [#13697](https://github.com/JabRef/jabref/pull/13697)

docs/requirements/cli.md

@@ -0,0 +1,14 @@
+---
+parent: Requirements
+---
+# CLI
+
+## Unified `--input` option across all commands
+`req~jabkit.cli.input-flag~1`
+
+All `jabkit` commands that need a file input must have the `--input` option to specify the input file.
+See [ADR 45](../decisions/0045-use-input-flag-always-for-input-files.md) for more details.
+
+Needs: impl
+
+<!-- markdownlint-disable-file MD022 -->

jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -41,7 +41,7 @@
         // sorted alphabetically
         subcommands = {
                 CheckConsistency.class,
-//                CheckIntegrity.class,
+                CheckIntegrity.class,
                 Convert.class,
                 Fetch.class,
                 GenerateBibFromAux.class,

jabkit/src/main/java/org/jabref/cli/CheckConsistency.java

@@ -33,6 +33,7 @@ class CheckConsistency implements Callable<Integer> {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
+    // [impl->req~jabkit.cli.input-flag~1]
     @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
     private Path inputFile;
 

jabkit/src/main/java/org/jabref/cli/CheckIntegrity.java

@@ -1,37 +1,117 @@
 package org.jabref.cli;
 
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
 import java.nio.file.Path;
+import java.util.List;
+import java.util.Locale;
+import java.util.Optional;
+import java.util.concurrent.Callable;
+import java.util.stream.Collectors;
 
 import org.jabref.cli.converter.CygWinPathConverter;
+import org.jabref.logic.importer.ParserResult;
+import org.jabref.logic.integrity.IntegrityCheck;
+import org.jabref.logic.integrity.IntegrityCheckResultCsvWriter;
+import org.jabref.logic.integrity.IntegrityCheckResultErrorFormatWriter;
+import org.jabref.logic.integrity.IntegrityCheckResultTxtWriter;
+import org.jabref.logic.integrity.IntegrityCheckResultWriter;
+import org.jabref.logic.integrity.IntegrityMessage;
+import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabaseContext;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import picocli.CommandLine;
 
 import static picocli.CommandLine.Command;
 import static picocli.CommandLine.Mixin;
 import static picocli.CommandLine.Option;
-import static picocli.CommandLine.Parameters;
 
 @Command(name = "check-integrity", description = "Check integrity of the database.")
-class CheckIntegrity implements Runnable {
+class CheckIntegrity implements Callable<Integer> {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(CheckIntegrity.class);
+
+    @CommandLine.ParentCommand
+    private ArgumentProcessor argumentProcessor;
 
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Parameters(index = "0", converter = CygWinPathConverter.class, description = "BibTeX file to check", arity = "0..1")
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
     private Path inputFile;
 
-    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file")
-    private Path inputOption;
+    @Option(names = {"--output-format"}, description = "Output format: errorformat, txt or csv", defaultValue = "errorformat")
+    private String outputFormat;
 
-    @Option(names = {"--output-format"}, description = "Output format: txt or csv")
-    private String outputFormat = "txt"; // FixMe: Default value?
+    // in BibTeX it could be preferences.getEntryEditorPreferences().shouldAllowIntegerEditionBibtex()
+    @Option(names = {"--allow-integer-edition"}, description = "Allows Integer edition", negatable = true, defaultValue = "true", fallbackValue = "true")
+    private boolean allowIntegerEdition;
 
     @Override
-    public void run() {
+    public Integer call() {
+        Optional<ParserResult> parserResult = ArgumentProcessor.importFile(
+                inputFile,
+                "bibtex",
+                argumentProcessor.cliPreferences,
+                sharedOptions.porcelain);
+        if (parserResult.isEmpty()) {
+            System.out.println(Localization.lang("Unable to open file '%0'.", inputFile));
+            return 2;
+        }
+
+        if (parserResult.get().isInvalid()) {
+            System.out.println(Localization.lang("Input file '%0' is invalid and could not be parsed.", inputFile));
+            return 2;
+        }
+
         if (!sharedOptions.porcelain) {
             System.out.println(Localization.lang("Checking integrity of '%0'.", inputFile));
             System.out.flush();
         }
 
-        // TODO: Implement integrity checking
+        BibDatabaseContext databaseContext = parserResult.get().getDatabaseContext();
+
+        IntegrityCheck integrityCheck = new IntegrityCheck(
+                databaseContext,
+                argumentProcessor.cliPreferences.getFilePreferences(),
+                argumentProcessor.cliPreferences.getCitationKeyPatternPreferences(),
+                JournalAbbreviationLoader.loadRepository(argumentProcessor.cliPreferences.getJournalAbbreviationPreferences()),
+                allowIntegerEdition
+        );
+
+        List<IntegrityMessage> messages = databaseContext.getEntries().stream()
+                .flatMap(entry -> integrityCheck.checkEntry(entry).stream())
+                .collect(Collectors.toList());
+
+        messages.addAll(integrityCheck.checkDatabase(databaseContext.getDatabase()));
+
+        Writer writer = new OutputStreamWriter(System.out);
+        IntegrityCheckResultWriter checkResultWriter;
+        switch (outputFormat.toLowerCase(Locale.ROOT)) {
+            case "errorformat" ->
+                    checkResultWriter = new IntegrityCheckResultErrorFormatWriter(writer, messages, parserResult.get(), inputFile);
+            case "txt" ->
+                    checkResultWriter = new IntegrityCheckResultTxtWriter(writer, messages);
+            case "csv" ->
+                    checkResultWriter = new IntegrityCheckResultCsvWriter(writer, messages);
+            default -> {
+                System.out.println(Localization.lang("Unknown output format '%0'.", outputFormat));
+                return 3;
+            }
+        }
+
+        try {
+            checkResultWriter.writeFindings();
+            writer.flush();
+        } catch (IOException e) {
+            LOGGER.error("Error writing results", e);
+            return 2;
+        }
+        return 0;
     }
 }

jabkit/src/main/java/org/jabref/cli/Convert.java

@@ -37,6 +37,7 @@ public class Convert implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
+    // [impl->req~jabkit.cli.input-flag~1]
     @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input file", required = true)
     private Path inputFile;
 

jabkit/src/main/java/org/jabref/cli/GenerateBibFromAux.java

@@ -5,6 +5,7 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.auxparser.AuxParser;
 import org.jabref.logic.auxparser.AuxParserResult;
 import org.jabref.logic.auxparser.AuxParserStatisticsProvider;
@@ -35,8 +36,9 @@ class GenerateBibFromAux implements Runnable {
     @Option(names = "--aux", required = true)
     private Path auxFile;
 
-    @Option(names = "--input", required = true)
-    private String inputFile;
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
     @Option(names = "--output")
     private Path outputFile;

jabkit/src/main/java/org/jabref/cli/GenerateCitationKeys.java

@@ -4,6 +4,7 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
@@ -28,8 +29,9 @@ public class GenerateCitationKeys implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Option(names = "--input", description = "The input .bib file.", required = true)
-    private String inputFile;
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
     @Option(names = "--output", description = "The output .bib file.")
     private Path outputFile;

jabkit/src/main/java/org/jabref/cli/PdfUpdate.java

@@ -9,6 +9,7 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.bibtex.FieldPreferences;
 import org.jabref.logic.exporter.EmbeddedBibFilePdfExporter;
@@ -49,8 +50,9 @@ class PdfUpdate implements Runnable {
     @Option(names = {"-k", "--citation-key"}, description = "Citation keys", required = true)
     private List<String> citationKeys = List.of(); // ToDo: check dedault value
 
-    @Option(names = "--input", description = "Input file", required = true)
-    private Path inputFile; // Local files only
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
     @Option(names = "--input-format", description = "Input format of the file", required = true)
     private String inputFormat = "*";

jabkit/src/main/java/org/jabref/cli/Search.java

@@ -47,6 +47,7 @@ class Search implements Runnable {
     @Option(names = {"--query"}, description = "Search query", required = true)
     private String query;
 
+    // [impl->req~jabkit.cli.input-flag~1]
     @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
     private Path inputFile;
 

jablib/src/main/java/org/jabref/logic/importer/ParserResult.java

@@ -4,7 +4,9 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.IdentityHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
@@ -14,6 +16,7 @@
 import org.jabref.model.database.BibDatabases;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryType;
+import org.jabref.model.entry.field.Field;
 import org.jabref.model.metadata.MetaData;
 
 public class ParserResult {
@@ -25,6 +28,9 @@ public class ParserResult {
     private boolean invalid;
     private boolean changedOnMigration = false;
 
+    private final Map<BibEntry, Range> articleRanges = new IdentityHashMap<>();
+    private final Map<BibEntry, Map<Field, Range>> fieldRanges = new IdentityHashMap<>();
+
     public ParserResult() {
         this(List.of());
     }
@@ -147,4 +153,16 @@ public boolean getChangedOnMigration() {
     public void setChangedOnMigration(boolean wasChangedOnMigration) {
         this.changedOnMigration = wasChangedOnMigration;
     }
+
+    public Map<BibEntry, Map<Field, Range>> getFieldRanges() {
+        return fieldRanges;
+    }
+
+    public Map<BibEntry, Range> getArticleRanges() {
+        return articleRanges;
+    }
+
+    public record Range(int startLine, int startColumn, int endLine, int endColumn) {
+        public static final Range NULL_RANGE = new Range(0, 0, 0, 0);
+    }
 }

jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -7,6 +7,7 @@
 import java.io.Reader;
 import java.io.StringWriter;
 import java.nio.file.Path;
+import java.util.ArrayDeque;
 import java.util.Base64;
 import java.util.Collection;
 import java.util.Deque;
@@ -46,6 +47,7 @@
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
 import org.jabref.model.entry.field.FieldProperty;
+import org.jabref.model.entry.field.InternalField;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.types.EntryTypeFactory;
 import org.jabref.model.groups.ExplicitGroup;
@@ -90,7 +92,7 @@
  */
 public class BibtexParser implements Parser {
     private static final Logger LOGGER = LoggerFactory.getLogger(BibtexParser.class);
-    private static final Integer LOOKAHEAD = 1024;
+    private static final int LOOKAHEAD = 1024;
     private static final String BIB_DESK_ROOT_GROUP_NAME = "BibDeskGroups";
     private static final DocumentBuilderFactory DOCUMENT_BUILDER_FACTORY = DocumentBuilderFactory.newInstance();
     private static final int INDEX_RELATIVE_PATH_IN_PLIST = 4;
@@ -100,7 +102,14 @@ public class BibtexParser implements Parser {
     private BibDatabase database;
     private Set<BibEntryType> entryTypes;
     private boolean eof;
+
     private int line = 1;
+    private int column = 1;
+    // Stores the last read column of the highest column number encountered on any line so far.
+    // The intended data structure is Stack, but it is not used because Java code style checkers complain.
+    // In basic JDK data structures, there is no size-limited stack. We did not want to include Apache Commons Collections only for "CircularFifoBuffer"
+    private final Deque<Integer> highestColumns = new ArrayDeque<>();
+
     private ParserResult parserResult;
     private final MetaDataParser metaDataParser;
     private final Map<String, String> parsedBibDeskGroups;
@@ -634,13 +643,20 @@ private int read() throws IOException {
         }
         if (character == '\n') {
             line++;
+            highestColumns.push(column);
+            column = 1;
+        } else {
+            column++;
         }
         return character;
     }
 
     private void unread(int character) throws IOException {
         if (character == '\n') {
             line--;
+            column = highestColumns.pop();
+        } else {
+            column--;
         }
         pushbackReader.unread(character);
         if (pureTextFromFile.getLast() == character) {
@@ -679,13 +695,22 @@ private String parsePreamble() throws IOException {
     private BibEntry parseEntry(String entryType) throws IOException {
         BibEntry result = new BibEntry(EntryTypeFactory.parse(entryType));
 
+        int articleStartLine = line;
+        int articleStartColumn = column;
+
         skipWhitespace();
         consume('{', '(');
         int character = peek();
         if ((character != '\n') && (character != '\r')) {
             skipWhitespace();
         }
+        int keyStartLine = line;
+        int keyStartColumn = column;
         String key = parseKey();
+
+        ParserResult.Range keyRange = new ParserResult.Range(keyStartLine, keyStartColumn, line, column);
+        parserResult.getFieldRanges().computeIfAbsent(result, _ -> new HashMap<>()).put(InternalField.KEY_FIELD, keyRange);
+
         result.setCitationKey(key);
         skipWhitespace();
 
@@ -713,10 +738,13 @@ private BibEntry parseEntry(String entryType) throws IOException {
         // Consume new line which signals end of entry
         skipOneNewline();
 
+        parserResult.getArticleRanges().put(result, new ParserResult.Range(articleStartLine, articleStartColumn, line, column));
         return result;
     }
 
     private void parseField(BibEntry entry) throws IOException {
+        int startLine = line;
+        int startColumn = column;
         Field field = FieldFactory.parseField(parseTextToken().toLowerCase(Locale.ROOT));
 
         skipWhitespace();
@@ -770,6 +798,8 @@ private void parseField(BibEntry entry) throws IOException {
                 }
             }
         }
+        ParserResult.Range keyRange = new ParserResult.Range(startLine, startColumn, line, column);
+        parserResult.getFieldRanges().computeIfAbsent(entry, _ -> new HashMap<>()).put(field, keyRange);
     }
 
     private String parseFieldContent(Field field) throws IOException {